The biotechnology of lactic acid bacteria with emphasis on applications in food safety and human health

Selostus: Terveyttä ja ruoan turvallisuutta edistävät maitohappobakteerien biotekniset sovellukset

Adaptive MCMC methods with applications in environmental and geophysical models

This work presents new, efficient Markov chain Monte Carlo (MCMC) simulation methods for statistical analysis in various modelling applications. When using MCMC methods, the model is simulated repeatedly to explore the probability distribution describing the uncertainties in model parameters and predictions. In adaptive MCMC methods based on the Metropolis-Hastings algorithm, the proposal distribution needed by the algorithm learns from the target distribution as the simulation proceeds. Adaptive MCMC methods have been subject of intensive research lately, as they open a way for essentially easier use of the methodology. The lack of user-friendly computer programs has been a main obstacle for wider acceptance of the methods. This work provides two new adaptive MCMC methods: DRAM and AARJ. The DRAM method has been built especially to work in high dimensional and non-linear problems. The AARJ method is an extension to DRAM for model selection problems, where the mathematical formulation of the model is uncertain and we want simultaneously to fit several different models to the same observations. The methods were developed while keeping in mind the needs of modelling applications typical in environmental sciences. The development work has been pursued while working with several application projects. The applications presented in this work are: a winter time oxygen concentration model for Lake Tuusulanjärvi and adaptive control of the aerator; a nutrition model for Lake Pyhäjärvi and lake management planning; validation of the algorithms of the GOMOS ozone remote sensing instrument on board the Envisat satellite of European Space Agency and the study of the effects of aerosol model selection on the GOMOS algorithm.

Sustainable Computer Science Education

As the world becomes more technologically advanced and economies become globalized, computer science evolution has become faster than ever before. With this evolution and globalization come the need for sustainable university curricula that adequately prepare graduates for life in the industry. Additionally, behavioural skills or “soft” skills have become just as important as technical abilities and knowledge or “hard” skills. The objective of this study was to investigate the current skill gap that exists between computer science university graduates and actual industry needs as well as the sustainability of current computer science university curricula by conducting a systematic literature review of existing publications on the subject as well as a survey of recently graduated computer science students and their work supervisors. A quantitative study was carried out with respondents from six countries, mainly Finland, 31 of the responses came from recently graduated computer science professionals and 18 from their employers. The observed trends suggest that a skill gap really does exist particularly with “soft” skills and that many companies are forced to provide additional training to newly graduated employees if they are to be successful at their jobs.

Embedding sustainability into the new computer science curriculum for English schools

The primary goals of this study are to: embed sustainable concepts of energy consumption into certain part of existing Computer Science curriculum for English schools; investigate how to motivate 7-to-11 years old kids to learn these concepts; promote responsive ICT (Information and Communications Technology) use by these kids in their daily life; raise their awareness of today’s ecological challenges. Sustainability-related ICT lessons developed aim to provoke computational thinking and creativity to foster understanding of environmental impact of ICT and positive environmental impact of small changes in user energy consumption behaviour. The importance of including sustainability into the Computer Science curriculum is due to the fact that ICT is both a solution and one of the causes of current world ecological problems. This research follows Agile software development methodology. In order to achieve the aforementioned goals, sustainability requirements, curriculum requirements and technical requirements are firstly analysed. Secondly, the web-based user interface is designed. In parallel, a set of three online lessons (video, slideshow and game) is created for the website GreenICTKids.com taking into account several green design patterns. Finally, the evaluation phase involves the collection of adults’ and kids’ feedback on the following: user interface; contents; user interaction; impacts on the kids’ sustainability awareness and on the kids’ behaviour with technologies. In conclusion, a list of research outcomes is as follows: 92% of the adults learnt more about energy consumption; 80% of the kids are motivated to learn about energy consumption and found the website easy to use; 100% of the kids understood the contents and liked website’s visual aspect; 100% of the kids will try to apply in their daily life what they learnt through the online lessons.

Wireless E-Business Applications in ICT Industry

Sähköisen liiketoiminnan sovelluksia on voitu toistaiseksi käyttää useimmissa tapauksissa vain langallisen yhteyden kautta. Uudet langattomat teknologiat, jotka ovat kehittyneet nopeasti muutaman viimeisen vuoden aikana, mahdollistavat näiden sovellusten käytön ajasta ja paikasta riippumatta. Tämän työn tavoitteena oli tutkia langattomien sähköisen liiketoiminnan sovellusten käyttöä ja hyötyjä tieto- ja viestintäteollisuudessa. Työssä keskitytään tutkimaan tätä tietotekniikan evoluutioaskelta yksittäisen yrityksen kannalta: rajoittuen omassa toiminnassa käytettäviin sovelluksiin. Tutkimus luo viitekehyksen mobiilisuuden evoluutioon, uuden tietotekniikan vaikutuksiin ja hyötyihin sekä tarkemmin langattomiin sähköisen liiketoiminnan sovelluksiin. Tätä viitekehystä käytetään analysoitaessa nykyistä käyttöä tutkimuksen kohteena olevissa yrityksissä. Tutkimuksen johtopäätökset niin nykyisestä käytöstä kuin myös tulevasta ovat syntyneet viitekehyksen, nykyisen käytön, sekä tehtyjen haastattelujen pohjalta.

The Future of Mobile Services and Wireless Applications in the Finnish Healthcare Sector

Työn päätavoitteena oli tutkia mobiilipalveluita ja langattomia sovelluksia Suomen terveydenhuollon sektorilla. Tutkimus havainnollistaa avain-alueita, missä mobiilipalvelut ja langattomat sovellukset voivat antaa lisäarvoa perinteiseen lääketieteen harjoittamiseen, ja selvittää, mitkä ovat tähän kehitykseen liittyvät suurimmat ongelmat ja uhkat sekä tutkimustuloksiin pohjautuvat mahdolliset palvelut ja sovellukset 5-10 vuoden kuluttua. Tutkimus oli luonteeltaan kvalitatiivinen ja tutkimuksen toteuttamiseen valittiin tulevaisuudentutkimus ja erityisesti yksi sen menetelmistä, delfoi-menetelmä. Tutkimuksen aineisto kerättiin kahdelta puolistrukturoidulta haastattelukierrokselta. Työn empiirinen osuus keskittyi kuvailemaan Suomen terveydenhuollon sektoria, siinä meneillään olevia projekteja sekä teknisiä esteitä. Lisäksi pyrittiin vastaamaan tutkimuksen pääkysymykseen. Tutkimustulokset osoittivat, että tärkeät alueet, joihin langaton kommunikaatio tulisi vaikuttamaan merkittävästi, ovat ensiaputoiminta, kroonisten potilaiden etämonitorointi, välineiden kehittäminen langattomaan kommunikaatioon kotihoidon parantamiseksi ja uusien toimintamallien luomiseksi sekä lääketieteellinen yhteistyö jakamalla terveydenhuoltoon liittyvät informaation lähteet. Työn tulosten perusteellavoitiin antaa myös muutamia toimenpide-ehdotuksia jatkotutkimuksia varten.

Inversion and assimilation methods with applications in geophysical remote sensing

Stratospheric ozone can be measured accurately using a limb scatter remote sensing technique at the UV-visible spectral region of solar light. The advantages of this technique includes a good vertical resolution and a good daytime coverage of the measurements. In addition to ozone, UV-visible limb scatter measurements contain information about NO2, NO3, OClO, BrO and aerosols. There are currently several satellite instruments continuously scanning the atmosphere and measuring the UVvisible region of the spectrum, e.g., the Optical Spectrograph and Infrared Imager System (OSIRIS) launched on the Odin satellite in February 2001, and the Scanning Imaging Absorption SpectroMeter for Atmospheric CartograpHY (SCIAMACHY) launched on Envisat in March 2002. Envisat also carries the Global Ozone Monitoring by Occultation of Stars (GOMOS) instrument, which also measures limb-scattered sunlight under bright limb occultation conditions. These conditions occur during daytime occultation measurements. The global coverage of the satellite measurements is far better than any other ozone measurement technique, but still the measurements are sparse in the spatial domain. Measurements are also repeated relatively rarely over a certain area, and the composition of the Earth’s atmosphere changes dynamically. Assimilation methods are therefore needed in order to combine the information of the measurements with the atmospheric model. In recent years, the focus of assimilation algorithm research has turned towards filtering methods. The traditional Extended Kalman filter (EKF) method takes into account not only the uncertainty of the measurements, but also the uncertainty of the evolution model of the system. However, the computational cost of full blown EKF increases rapidly as the number of the model parameters increases. Therefore the EKF method cannot be applied directly to the stratospheric ozone assimilation problem. The work in this thesis is devoted to the development of inversion methods for satellite instruments and the development of assimilation methods used with atmospheric models.

Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

Promoting Programming Learning. Engagement, Automatic Assessment with Immediate Feedback in Visualizations

The skill of programming is a key asset for every computer science student. Many studies have shown that this is a hard skill to learn and the outcomes of programming courses have often been substandard. Thus, a range of methods and tools have been developed to assist students’ learning processes. One of the biggest fields in computer science education is the use of visualizations as a learning aid and many visualization based tools have been developed to aid the learning process during last few decades. Studies conducted in this thesis focus on two different visualizationbased tools TRAKLA2 and ViLLE. This thesis includes results from multiple empirical studies about what kind of effects the introduction and usage of these tools have on students’ opinions and performance, and what kind of implications there are from a teacher’s point of view. The results from studies in this thesis show that students preferred to do web-based exercises, and felt that those exercises contributed to their learning. The usage of the tool motivated students to work harder during their course, which was shown in overall course performance and drop-out statistics. We have also shown that visualization-based tools can be used to enhance the learning process, and one of the key factors is the higher and active level of engagement (see. Engagement Taxonomy by Naps et al., 2002). The automatic grading accompanied with immediate feedback helps students to overcome obstacles during the learning process, and to grasp the key element in the learning task. These kinds of tools can help us to cope with the fact that many programming courses are overcrowded with limited teaching resources. These tools allows us to tackle this problem by utilizing automatic assessment in exercises that are most suitable to be done in the web (like tracing and simulation) since its supports students’ independent learning regardless of time and place. In summary, we can use our course’s resources more efficiently to increase the quality of the learning experience of the students and the teaching experience of the teacher, and even increase performance of the students. There are also methodological results from this thesis which contribute to developing insight into the conduct of empirical evaluations of new tools or techniques. When we evaluate a new tool, especially one accompanied with visualization, we need to give a proper introduction to it and to the graphical notation used by tool. The standard procedure should also include capturing the screen with audio to confirm that the participants of the experiment are doing what they are supposed to do. By taken such measures in the study of the learning impact of visualization support for learning, we can avoid drawing false conclusion from our experiments. As computer science educators, we face two important challenges. Firstly, we need to start to deliver the message in our own institution and all over the world about the new – scientifically proven – innovations in teaching like TRAKLA2 and ViLLE. Secondly, we have the relevant experience of conducting teaching related experiment, and thus we can support our colleagues to learn essential know-how of the research based improvement of their teaching. This change can transform academic teaching into publications and by utilizing this approach we can significantly increase the adoption of the new tools and techniques, and overall increase the knowledge of best-practices. In future, we need to combine our forces and tackle these universal and common problems together by creating multi-national and multiinstitutional research projects. We need to create a community and a platform in which we can share these best practices and at the same time conduct multi-national research projects easily.

Enabling constructive alignment in programming instruction

In this thesis, simple methods have been sought to lower the teacher’s threshold to start to apply constructive alignment in instruction. From the phases of the instructional process, aspects that can be improved with little effort by the teacher have been identified. Teachers have been interviewed in order to find out what students actually learn in computer science courses. A quantitative analysis of the structured interviews showed that in addition to subject specific skills and knowledge, students learn many other skills that should be mentioned in the learning outcomes of the course. The students’ background, such as their prior knowledge, learning style and culture, affects how they learn in a course. A survey was conducted to map the learning styles of computer science students and to see if their cultural background affected their learning style. A statistical analysis of the data indicated that computer science students are different learners than engineering students in general and that there is a connection between the student’s culture and learning style. In this thesis, a simple self-assessment scale that is based on Bloom’s revised taxonomy has been developed. A statistical analysis of the test results indicates that in general the scale is quite reliable, but single students still slightly overestimate or under-estimate their knowledge levels. For students, being able to follow their own progress is motivating, and for a teacher, self-assessment results give information about how the class is proceeding and what the level of the students’ knowledge is.

Kahden merkkijonon pisimmän yhteisen alijonon ongelma ja sen ratkaiseminen

Tämä tutkielma kuuluu merkkijonoalgoritmiikan piiriin. Merkkijono S on merkkijonojen X[1..m] ja Y[1..n] yhteinen alijono, mikäli se voidaan muodostaa poistamalla X:stä 0..m ja Y:stä 0..n kappaletta merkkejä mielivaltaisista paikoista. Jos yksikään X:n ja Y:n yhteinen alijono ei ole S:ää pidempi, sanotaan, että S on X:n ja Y:n pisin yhteinen alijono (lyh. PYA). Tässä työssä keskitytään kahden merkkijonon PYAn ratkaisemiseen, mutta ongelma on yleistettävissä myös useammalle jonolle. PYA-ongelmalle on sovelluskohteita – paitsi tietojenkäsittelytieteen niin myös bioinformatiikan osa-alueilla. Tunnetuimpia niistä ovat tekstin ja kuvien tiivistäminen, tiedostojen versionhallinta, hahmontunnistus sekä DNA- ja proteiiniketjujen rakennetta vertaileva tutkimus. Ongelman ratkaisemisen tekee hankalaksi ratkaisualgoritmien riippuvuus syötejonojen useista eri parametreista. Näitä ovat syötejonojen pituuden lisäksi mm. syöttöaakkoston koko, syötteiden merkkijakauma, PYAn suhteellinen osuus lyhyemmän syötejonon pituudesta ja täsmäävien merkkiparien lukumäärä. Täten on vaikeaa kehittää algoritmia, joka toimisi tehokkaasti kaikille ongelman esiintymille. Tutkielman on määrä toimia yhtäältä käsikirjana, jossa esitellään ongelman peruskäsitteiden kuvauksen jälkeen jo aikaisemmin kehitettyjä tarkkoja PYAalgoritmeja. Niiden tarkastelu on ryhmitelty algoritmin toimintamallin mukaan joko rivi, korkeuskäyrä tai diagonaali kerrallaan sekä monisuuntaisesti prosessoiviin. Tarkkojen menetelmien lisäksi esitellään PYAn pituuden ylä- tai alarajan laskevia heuristisia menetelmiä, joiden laskemia tuloksia voidaan hyödyntää joko sellaisinaan tai ohjaamaan tarkan algoritmin suoritusta. Tämä osuus perustuu tutkimusryhmämme julkaisemiin artikkeleihin. Niissä käsitellään ensimmäistä kertaa heuristiikoilla tehostettuja tarkkoja menetelmiä. Toisaalta työ sisältää laajahkon empiirisen tutkimusosuuden, jonka tavoitteena on ollut tehostaa olemassa olevien tarkkojen algoritmien ajoaikaa ja muistinkäyttöä. Kyseiseen tavoitteeseen on pyritty ohjelmointiteknisesti esittelemällä algoritmien toimintamallia hyvin tukevia tietorakenteita ja rajoittamalla algoritmien suorittamaa tuloksetonta laskentaa parantamalla niiden kykyä havainnoida suorituksen aikana saavutettuja välituloksia ja hyödyntää niitä. Tutkielman johtopäätöksinä voidaan yleisesti todeta tarkkojen PYA-algoritmien heuristisen esiprosessoinnin lähes systemaattisesti pienentävän niiden suoritusaikaa ja erityisesti muistintarvetta. Lisäksi algoritmin käyttämällä tietorakenteella on ratkaiseva vaikutus laskennan tehokkuuteen: mitä paikallisempia haku- ja päivitysoperaatiot ovat, sitä tehokkaampaa algoritmin suorittama laskenta on.

Structural and operational optimisation : applications in energy systems

In this work mathematical programming models for structural and operational optimisation of energy systems are developed and applied to a selection of energy technology problems. The studied cases are taken from industrial processes and from large regional energy distribution systems. The models are based on Mixed Integer Linear Programming (MILP), Mixed Integer Non-Linear Programming (MINLP) and on a hybrid approach of a combination of Non-Linear Programming (NLP) and Genetic Algorithms (GA). The optimisation of the structure and operation of energy systems in urban regions is treated in the work. Firstly, distributed energy systems (DES) with different energy conversion units and annual variations of consumer heating and electricity demands are considered. Secondly, district cooling systems (DCS) with cooling demands for a large number of consumers are studied, with respect to a long term planning perspective regarding to given predictions of the consumer cooling demand development in a region. The work comprises also the development of applications for heat recovery systems (HRS), where paper machine dryer section HRS is taken as an illustrative example. The heat sources in these systems are moist air streams. Models are developed for different types of equipment price functions. The approach is based on partitioning of the overall temperature range of the system into a number of temperature intervals in order to take into account the strong nonlinearities due to condensation in the heat recovery exchangers. The influence of parameter variations on the solutions of heat recovery systems is analysed firstly by varying cost factors and secondly by varying process parameters. Point-optimal solutions by a fixed parameter approach are compared to robust solutions with given parameter variation ranges. In the work enhanced utilisation of excess heat in heat recovery systems with impingement drying, electricity generation with low grade excess heat and the use of absorption heat transformers to elevate a stream temperature above the excess heat temperature are also studied.

Carbon sources for Power-to-Gas applications in the Finnish energy system

This thesis is done as a part of the NEOCARBON project. The aim of NEOCARBON project is to study a fully renewable energy system utilizing Power-to-Gas or Power-to-Liquid technology for energy storage. Power-to-Gas consists of two main operations: Hydrogen production via electrolysis and methane production via methanation. Methanation requires carbon dioxide and hydrogen as a raw material. This thesis studies the potential carbon dioxide sources within Finland. The different sources are ranked using the cost and energy penalty of the carbon capture, carbon biogenity and compatibility with Power-to-Gas. It can be concluded that in Finland there exists enough CO2 point sources to provide national PtG system with sufficient amounts of carbon. Pulp and paper industry is single largest producer of biogenic CO2 in Finland. It is possible to obtain single unit capable of grid balancing operations and energy transformations via Power-to-Gas and Gas-to-Power by coupling biogas plants with biomethanation and CHP units.

The role of business model in computer game development organizations

The computer game industry has grown steadily for years, and in revenues it can be compared to the music and film industries. The game industry has been moving to digital distribution. Computer gaming and the concept of business model are discussed among industrial practitioners and the scientific community. The significance of the business model concept has increased in the scientific literature recently, although there is still a lot of discussion going on on the concept. In the thesis, the role of the business model in the computer game industry is studied. Computer game developers, designers, project managers and organization leaders in 11 computer game companies were interviewed. The data was analyzed to identify the important elements of computer game business model, how the business model concept is perceived and how the growth of the organization affects the business model. It was identified that the importance of human capital is crucial to the business. As games are partly a product of creative thinking also innovation and the creative process are highly valued. The same applies to technical skills when performing various activities. Marketing and customer relationships are also considered as key elements in the computer game business model. Financing and partners are important especially for startups, when the organization is dependent on external funding and third party assets. The results of this study provide organizations with improved understanding on how the organization is built and what business model elements are weighted.